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Metagenome-wide association studies have led to the discovery of potential interactions between the microbiome and urolithiasis, but a lack of standardization has raised questions about the reproducibility, applicability and physiological relevance of metagenome-wide association study data. This Consensus Statement describes the formation of the first international consortium for microbiome in urinary stone disease — MICROCOSM — and the outcomes of a consensus meeting to develop standardized protocols for microbiome studies and generate a data repository, which are both publicly available via a secure online server.